Package 'MSnbase'

Description

These methods add identification data to a raw MS experiment (an "MSnExp" object) or to quantitative data (an "MSnSet" object). The identification data needs to be available as a mzIdentML file (and passed as filenames, or directly as identification object) or, alternatively, can be passed as an arbitrary data.frame. See details in the Methods section.

Details

The featureData slots in a "MSnExp" or a "MSnSet" instance provides only one row per MS2 spectrum but the identification is not always bijective. Prior to addition, the identification data is filtered as documented in the filterIdentificationDataFrame function: (1) only PSMs matching the regular (non-decoy) database are retained; (2) PSMs of rank greater than 1 are discarded; and (3) only proteotypic peptides are kept.

If after filtering, more then one PSM per spectrum are still present, these are combined (reduced, see reduce,data.frame-method) into a single row and separated by a semi-colon. This has as side-effect that feature variables that are being reduced are converted to characters. See the reduce manual page for examples.

See also the section about identification data in the MSnbase-demo vignette for details and additional examples.

After addition of the identification data, new feature variables are created. The column nprot contains the number of members in the protein group; the columns accession and description contain a semicolon separated list of all matches. The columns npsm.prot and npep.prot represent the number of PSMs and peptides that were matched to a particular protein group. The column npsm.pep indicates how many PSMs were attributed to a peptide (as defined by its sequence pepseq). All these values are re-calculated after filtering and reduction.

Methods

signature(object = "MSnExp", id = "character", ...

Adds the identification data stored in mzIdentML files to a "MSnExp" instance. The method handles one or multiple mzIdentML files provided via id. id has to be a character vector of valid filenames. See below for additional arguments.

signature(object = "MSnExp", id = "mzID", ...)

Same as above but id is a mzID object generated by mzID::mzID. See below for additional arguments.

signature(object = "MSnExp", id = "mzIDCollection", ...)

Same as above but id is a mzIDCollection object. See below for additional arguments.

signature(object = "MSnExp", id = "mzRident", ...

Same as above but id is a mzRident object generated by mzR::openIdfile. See below for additional arguments.

signature(object = "MSnExp", id = "data.frame", ...

Same as above but id could be a data.frame. See below for additional arguments.

signature(object = "MSnSet", id = "character", ...)

Adds the identification data stored in mzIdentML files to an "MSnSet" instance. The method handles one or multiple mzIdentML files provided via id. id has to be a character vector of valid filenames. See below for additional arguments.

signature(object = "MSnSet", id = "mzID", ...)

Same as above but id is a mzID object. See below for additional arguments.

signature(object = "MSnSet", id = "mzIDCollection", ...)

Same as above but id is a mzIDCollection object. See below for additional arguments.

signature(object = "MSnSet", id = "data.frame", ...)

Same as above but id is a data.frame. See below for additional arguments.

The methods above take the following additional argument. These need to be set when adding identification data as a data.frame. In all other cases, the defaults are set automatically.

fcol

The matching between the features (raw spectra or quantiative features) and identification results is done by matching columns in the featue data (the featureData slot) and the identification data. These values are the spectrum file index and the acquisition number, passed as a character of length 2. The default values for these variables in the object's feature data are "spectrum.file" and "acquisition.num". Values need to be provided when id is a data.frame.

icol

The default values for the spectrum file and acquisition numbers in the identification data (the id argument) are "spectrumFile" and "acquisitionNum". Values need to be provided when id is a data.frame.

acc

The protein (group) accession number or identifier. Defaults are "DatabaseAccess" when passing filenames or mzRident objects and "accession" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

desc

The protein (group) description. Defaults are "DatabaseDescription" when passing filenames or mzRident objects and "description" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

pepseq

The peptide sequence variable name. Defaults are "sequence" when passing filenames or mzRident objects and "pepseq" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

key

The key to be used when the identification data need to be reduced (see details section). Defaults are "spectrumID" when passing filenames or mzRident objects and "spectrumid" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame.

decoy

The feature variable used to define whether the PSM was matched in the decoy of regular fasta database for PSM filtering. Defaults are "isDecoy" when passing filenames or mzRident objects and "isdecoy" when passing mzID or mzIDCollection objects. A value needs to be provided when id is a data.frame. See filterIdentificationDataFrame for details.

rank

The feature variable used to defined the rank of the PSM for filtering. Defaults is "rank". A value needs to be provided when id is a data.frame. See filterIdentificationDataFrame for details.

accession

The feature variable used to defined the protein (groupo) accession or identifier for PSM filterin. Defaults is to use the same value as acc . A value needs to be provided when id is a data.frame. See filterIdentificationDataFrame for details.

verbose

A logical defining whether to print out messages or not. Default is to use the session-wide open from isMSnbaseVerbose.

Author(s)

Sebastian Gibb <[email protected]> and Laurent Gatto

See Also

filterIdentificationDataFrame for the function that filters identification data, readMzIdData to read the identification data as a unfiltered data.frame and reduce,data.frame-method to reduce it to a data.frame that contains only unique PSMs per row.

Examples

## find path to a mzXML file
quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                 full.name = TRUE, pattern = "mzXML$")
## find path to a mzIdentML file
identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                 full.name = TRUE, pattern = "dummyiTRAQ.mzid")

## create basic MSnExp
msexp <- readMSData(quantFile)

## add identification information
msexp <- addIdentificationData(msexp, identFile)

## access featureData
fData(msexp)

idSummary(msexp)

Description

This function evaluates the variability within all protein group of an MSnSet. If a protein group is composed only of a single feature, NA is returned.

Usage

aggvar(object, groupBy, fun)

Arguments

Details

This function can be used to identify protein groups with incoherent feature (petides or PSMs) expression patterns. Using max as a function, one can identify protein groups with single extreme outliers, such as, for example, a mis-identified peptide that was erroneously assigned to that protein group. Using mean identifies more systematic inconsistencies where, for example, the subsets of peptide (or PSM) feautres correspond to proteins with different expression patterns.

Value

A matrix providing the number of features per protein group (nb_feats column) and the aggregation summarising distance (agg_dist column).

Author(s)

Laurent Gatto

See Also

combineFeatures to combine PSMs quantitation into peptides and/or into proteins.

Examples

library("pRolocdata")
data(hyperLOPIT2015ms3r1psm)
groupBy <- "Protein.Group.Accessions"
res1 <- aggvar(hyperLOPIT2015ms3r1psm, groupBy, fun = max)
res2 <- aggvar(hyperLOPIT2015ms3r1psm, groupBy, fun = mean)
par(mfrow = c(1, 3))
plot(res1, log = "y", main = "Single outliers (max)")
plot(res2, log = "y", main = "Overall inconsistency (mean)")
plot(res1[, "agg_dist"], res2[, "agg_dist"],
     xlab = "max", ylab = "mean")

Description

A function to convert the identification data contained in an mzRident object to a data.frame. Each row represents a scan, which can however be repeated several times if the PSM matches multiple proteins and/or contains two or more modifications. To reduce the data.frame so that rows/scans are unique and use semicolon-separated values to combine information pertaining a scan, use reduce.

Arguments

Details

See also the Tandem MS identification data section in the MSnbase-demo vignette.

Value

A data.frame

Author(s)

Laurent Gatto

Examples

## find path to a mzIdentML file
identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                 full.name = TRUE, pattern = "dummyiTRAQ.mzid")
library("mzR")
x <- openIDfile(identFile)
x
as(x, "data.frame")

Description

Given a list of MSnSet instances, typically representing replicated experiments, the function returns an average MSnSet.

Usage

averageMSnSet(x, avg = function(x) mean(x, na.rm = TRUE), disp = npcv)

Arguments

Details

This function is aimed at facilitating the visualisation of replicated experiments and should not be used as a replacement for a statistical analysis.

The samples of the instances to be averaged must be identical but can be in a different order (they will be reordered by default). The features names of the result will correspond to the union of the feature names of the input MSnSet instances. Each average value will be computed by the avg function and the dispersion of the replicated measurements will be estimated by the disp function. These dispersions will be stored as a data.frame in the feature metadata that can be accessed with fData(.)$disp. Similarly, the number of missing values that were present when average (and dispersion) were computed are available in fData(.)$disp.

Currently, the feature metadata of the returned object corresponds the the feature metadata of the first object in the list (augmented with the missing value and dispersion values); the metadata of the features that were missing in this first input are missing (i.e. populated with NAs). This may change in the future.

Value

A new average MSnSet.

Author(s)

Laurent Gatto

See Also

compfnames to compare MSnSet feature names.

Examples

library("pRolocdata")
## 3 replicates from Tan et al. 2009
data(tan2009r1)
data(tan2009r2)
data(tan2009r3)
x <- MSnSetList(list(tan2009r1, tan2009r2, tan2009r3))
avg <- averageMSnSet(x)
dim(avg)
head(exprs(avg))
head(fData(avg)$nNA)
head(fData(avg)$disp)
## using the standard deviation as measure of dispersion
avg2 <-averageMSnSet(x, disp = sd)
head(fData(avg2)$disp)
## keep only complete observations, i.e proteins 
## that had 0 missing values for all samples
sel <- apply(fData(avg)$nNA, 1 , function(x) all(x == 0))
avg <- avg[sel, ]
disp <- rowMax(fData(avg)$disp)
library("pRoloc")
setStockcol(paste0(getStockcol(), "AA"))
plot2D(avg, cex = 7.7 * disp)
title(main = paste("Dispersion: non-parametric CV",
                   paste(round(range(disp), 3), collapse = " - ")))

Description

This method aggregates individual spectra (Spectrum instances) or whole experiments (MSnExp instances) into discrete bins. All intensity values which belong to the same bin are summed together.

Methods

signature(object = "MSnExp", binSize = "numeric", verbose = "logical")

Bins all spectra in an MSnExp object. Use binSize to control the size of a bin (in Dalton, default is 1). Displays a control bar if verbose set to TRUE (default). Returns a binned MSnExp instance.

signature(object = "Spectrum", binSize = "numeric", breaks = "numeric", msLevel. = "numeric")

Bin the Spectrum object. Use binSize to control the size of a bin (in Dalton, default is 1). Similar to hist you could use breaks to specify the breakpoints between m/z bins. msLevel. defines the level of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

Returns a binned Spectrum instance.

Author(s)

Sebastian Gibb <[email protected]>

See Also

clean, pickPeaks, smooth, removePeaks and trimMz for other spectra processing methods.

Examples

s <- new("Spectrum2", mz=1:10, intensity=1:10)
intensity(s)
intensity(bin(s, binSize=2))

data(itraqdata)
sum(peaksCount(itraqdata))
itraqdata2 <- bin(itraqdata, binSize=2)
sum(peaksCount(itraqdata2))
processingData(itraqdata2)

Description

These method calculates a-, b-, c-, x-, y- and z-ions produced by fragmentation.

Arguments

Methods

signature(sequence = "character", object = "missing", ...)

Calculates the theoretical fragments for a peptide sequence. Returns a data.frame with the columns c("mz", "ion", "type", "pos", "z", "seq").

signature(sequence = "character", object = "Spectrum2", ...)

Calculates and matches the theoretical fragments for a peptide sequence and a "Spectrum2" object. The ... arguments are passed to the internal functions. Currently tolerance, method and relative are supported.

You could change the tolerance (default 0.1) and decide whether this tolerance should be applied relative to the target m/z (relative = TRUE) or absolute (default relative = FALSE) to match the theoretical fragment MZ with the MZ of the spectrum. When (relative = TRUE) the mass tolerance window is set to target mz +/- (target mz * tolerance) and target mz +/- tolerance otherwise. In cases of multiple matches use method to select the peak with the highest intensity (method = "highest", default) respectively closest MZ (method = "closes"). If method = "all" is set all possible matches in the current tolerance range are reported. Returns the same data.frame as above but the mz column represents the matched MZ values of the spectrum. Additionally there is a column error that contains the difference between the observed MZ (from the spectrum) to the theoretical fragment MZ.

Author(s)

Sebastian Gibb <[email protected]>

Examples

## find path to a mzXML file
file <- dir(system.file(package = "MSnbase", dir = "extdata"),
            full.name = TRUE, pattern = "mzXML$")

## create basic MSnExp
msexp <- readMSData(file, centroided = FALSE)

## centroid them
msexp <- pickPeaks(msexp)

## calculate fragments for ACE with default modification
calculateFragments("ACE", modifications=c(C=57.02146))

## calculate fragments for ACE with an addition N-terminal modification
calculateFragments("ACE", modifications=c(C=57.02146, Nterm=229.1629))

## calculate fragments for ACE without any modifications
calculateFragments("ACE", modifications=NULL)

calculateFragments("VESITARHGEVLQLRPK",
                   type=c("a", "b", "c", "x", "y", "z"),
                   z=1:2)

calculateFragments("VESITARHGEVLQLRPK", msexp[[1]])

## neutral loss
PSMatch::defaultNeutralLoss()

## disable water loss on the C terminal
PSMatch::defaultNeutralLoss(disableWaterLoss="Cterm")

## real example
calculateFragments("PQR")
calculateFragments("PQR",
                   neutralLoss=PSMatch::defaultNeutralLoss(disableWaterLoss="Cterm"))
calculateFragments("PQR",
                   neutralLoss=PSMatch::defaultNeutralLoss(disableAmmoniaLoss="Q"))

## disable neutral loss completely
calculateFragments("PQR", neutralLoss=NULL)

Description

The Chromatogram class is designed to store chromatographic MS data, i.e. pairs of retention time and intensity values. Instances of the class can be created with the Chromatogram constructor function but in most cases the dedicated methods for OnDiskMSnExp and MSnExp objects extracting chromatograms should be used instead (i.e. the chromatogram() method).

Usage

Chromatogram(
  rtime = numeric(),
  intensity = numeric(),
  mz = c(NA_real_, NA_real_),
  filterMz = c(NA_real_, NA_real_),
  precursorMz = c(NA_real_, NA_real_),
  productMz = c(NA_real_, NA_real_),
  fromFile = integer(),
  aggregationFun = character(),
  msLevel = 1L
)

aggregationFun(object)

## S4 method for signature 'Chromatogram'
show(object)

## S4 method for signature 'Chromatogram'
rtime(object)

## S4 method for signature 'Chromatogram'
intensity(object)

## S4 method for signature 'Chromatogram'
mz(object, filter = FALSE)

## S4 method for signature 'Chromatogram'
precursorMz(object)

## S4 method for signature 'Chromatogram'
fromFile(object)

## S4 method for signature 'Chromatogram'
length(x)

## S4 method for signature 'Chromatogram'
as.data.frame(x)

## S4 method for signature 'Chromatogram'
filterRt(object, rt)

## S4 method for signature 'Chromatogram'
clean(object, all = FALSE, na.rm = FALSE)

## S4 method for signature 'Chromatogram,ANY'
plot(
  x,
  col = "#00000060",
  lty = 1,
  type = "l",
  xlab = "retention time",
  ylab = "intensity",
  main = NULL,
  ...
)

## S4 method for signature 'Chromatogram'
msLevel(object)

## S4 method for signature 'Chromatogram'
isEmpty(x)

## S4 method for signature 'Chromatogram'
productMz(object)

## S4 method for signature 'Chromatogram'
bin(
  x,
  binSize = 0.5,
  breaks = seq(floor(min(rtime(x))), ceiling(max(rtime(x))), by = binSize),
  fun = max
)

## S4 method for signature 'Chromatogram'
normalize(object, method = c("max", "sum"))

## S4 method for signature 'Chromatogram'
filterIntensity(object, intensity = 0, ...)

## S4 method for signature 'Chromatogram,Chromatogram'
alignRt(x, y, method = c("closest", "approx"), ...)

## S4 method for signature 'Chromatogram,Chromatogram'
compareChromatograms(
  x,
  y,
  ALIGNFUN = alignRt,
  ALIGNFUNARGS = list(),
  FUN = cor,
  FUNARGS = list(use = "pairwise.complete.obs"),
  ...
)

## S4 method for signature 'Chromatogram'
transformIntensity(object, FUN = identity)

Arguments

Details

The mz, filterMz, precursorMz and productMz are stored as a numeric(2) representing a range even if the chromatogram was generated for only a single ion (i.e. a single mz value). Using ranges for mz values allow this class to be used also for e.g. total ion chromatograms or base peak chromatograms.

The slots `precursorMz` and `productMz` allow to represent SRM
(single reaction monitoring) and MRM (multiple SRM) chromatograms. As
example, a `Chromatogram` for a SRM transition 273 -> 153 will have
a `@precursorMz = c(273, 273)` and a
`@productMz = c(153, 153)`.

Object creation

Chromatogram objects can be extracted from an MSnExp or OnDiskMSnExp object with the chromatogram() function.

Alternatively, the constructor function Chromatogram can be used, which takes arguments rtime, intensity, mz, filterMz, precursorMz, productMz, fromFile, aggregationFun and msLevel.

Data access and coercion

• aggregationFun: gets the aggregation function used to create the Chromatogram.

• as.data.frame: returns a data.frame with columns "rtime" and "intensity".

• fromFile: returns an integer(1) with the index of the originating file.

• intensity: returns the intensities from the Chromatogram.

• isEmpty: returns TRUE if the chromatogram is empty or has only NA intensities.

• length: returns the length (i.e. number of data points) of the Chromatogram.

• msLevel: returns an integer(1) with the MS level of the chromatogram.

• mz: get the m/z (range) from the Chromatogram. The function returns a numeric(2) with the lower and upper boundaries. Parameter filter allows to specify whether the m/z range used to filter the originating object should be returned or the m/z range of the actual data.

• precursorMz: get the m/z of the precursor ion. The function returns a numeric(2) with the lower and upper boundary.

• productMz: get the m/z of the producto chromatogram/ion. The function returns a numeric(2) with the lower and upper m/z value.

• rtime: returns the retention times from the Chromatogram.

Data subsetting and filtering

• filterRt: filter/subset the Chromatogram to the specified retention time range (defined with parameter rt).

• filterIntensity: filter a Chromatogram() object removing data points with intensities below a user provided threshold. If intensity is a numeric value, the returned chromatogram will only contain data points with intensities > intensity. In addition it is possible to provide a function to perform the filtering. This function is expected to take the input Chromatogram (object) and to return a logical vector with the same length then there are data points in object with TRUE for data points that should be kept and FALSE for data points that should be removed. See examples below.

Data processing and manipulation

• alignRt: Aligns chromatogram x against chromatogram y. The resulting chromatogram has the same length (number of data points) than y and the same retention times thus allowing to perform any pair-wise comparisons between the chromatograms. If x is a MChromatograms() object, each Chromatogram in it is aligned against y. Additional parameters (...) are passed along to the alignment functions (e.g. closest()).

  Parameter method allows to specify which alignment method should be used. Currently there are the following options:

  • method = "closest" (the default): match data points in the first chromatogram (x) to those of the second (y) based on the difference between their retention times: each data point in x is assigned to the data point in y with the smallest difference in their retention times if their difference is smaller than the minimum average difference between retention times in x or y (parameter tolerance for the call to the closest() function). By setting tolerance = 0 only exact retention times are matched against each other (i.e. only values are kept with exactly the same retention times between both chromatograms).

  • method = "approx": uses the base R approx function to approximate intensities in x to the retention times in y (using linear interpolation). This should only be used for chromatograms that were measured in the same measurement run (e.g. MS1 and corresponding MS2 chromatograms from SWATH experiments).

• bin: aggregates intensity values from a chromatogram in discrete bins along the retention time axis and returns a Chromatogram object with the retention time representing the mid-point of the bins and the intensity the binned signal. Parameters binSize and breaks allow to define the binning, fun the function which should be used to aggregate the intensities within a bin.

• compareChromatograms: calculates a similarity score between 2 chromatograms after aligning them. Parameter ALIGNFUN allows to define a function that can be used to align x against y (defaults to ALIGNFUN = alignRt). Subsequently, the similarity is calculated on the aligned intensities with the function provided with parameter FUN which defaults to cor (hence by default the Pearson correlation is calculated between the aligned intensities of the two compared chromatograms). Additional parameters can be passed to the ALIGNFUN and FUN with the parameter ALIGNFUNARGS and FUNARGS, respectively.

• clean: removes 0-intensity data points (and NA values). See clean() for details.

• normalize, normalise: normalises the intensities of a chromatogram by dividing them either by the maximum intensity (method = "max") or total intensity (method = "sum") of the chromatogram.

• transformIntensity: allows to manipulate the intensity values of a chromatogram using a user provided function. See below for examples.

Data visualization

• plot: plots a Chromatogram object.

Author(s)

Johannes Rainer

See Also

MChromatograms for combining Chromatogram in a two-dimensional matrix (rows being mz-rt ranges, columns samples). ⁠chromatogram()] for the method to extract chromatogram data from an ⁠MSnExporOnDiskMSnExp⁠object. [clean()] for the method to *clean* a⁠Chromatogram' object.

Examples

## Create a simple Chromatogram object.
ints <- abs(rnorm(100, sd = 100))
rts <- seq_len(length(ints))
chr <- Chromatogram(rtime = rts, intensity = ints)
chr

## Extract intensities
intensity(chr)

## Extract retention times
rtime(chr)

## Extract the mz range - is NA for the present example
mz(chr)

## plot the Chromatogram
plot(chr)

## Create a simple Chromatogram object based on random values.
chr <- Chromatogram(intensity = abs(rnorm(1000, mean = 2000, sd = 200)),
        rtime = sort(abs(rnorm(1000, mean = 10, sd = 5))))
chr

## Get the intensities
head(intensity(chr))

## Get the retention time
head(rtime(chr))

## What is the retention time range of the object?
range(rtime(chr))

## Filter the chromatogram to keep only values between 4 and 10 seconds
chr2 <- filterRt(chr, rt = c(4, 10))

range(rtime(chr2))

## Data manipulations:

## normalize a chromatogram
par(mfrow = c(1, 2))
plot(chr)
plot(normalize(chr, method = "max"))

## Align chromatograms against each other

chr1 <- Chromatogram(rtime = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
    intensity = c(3, 5, 14, 30, 24, 6, 2, 1, 1, 0))
chr2 <- Chromatogram(rtime = c(2.5, 3.42, 4.5, 5.43, 6.5),
    intensity = c(5, 12, 15, 11, 5))

plot(chr1, col = "black")
points(rtime(chr2), intensity(chr2), col = "blue", type = "l")

## Align chr2 to chr1 without interpolation
res <- alignRt(chr2, chr1)
rtime(res)
intensity(res)
points(rtime(res), intensity(res), col = "#00ff0080", type = "l")

## Align chr2 to chr1 with interpolation
res <- alignRt(chr2, chr1, method = "approx")
points(rtime(res), intensity(res), col = "#ff000080", type = "l")
legend("topright", col = c("black", "blue", "#00ff0080","#ff000080"),lty = 1,
    legend = c("chr1", "chr2", "chr2 matchRtime", "chr2 approx"))


## Compare Chromatograms. Align chromatograms with `alignRt` and
## method `"approx"`
compareChromatograms(chr2, chr1, ALIGNFUNARGS = list(method = "approx"))

## Data filtering

chr1 <- Chromatogram(rtime = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
    intensity = c(3, 5, 14, 30, 24, 6, 2, 1, 1, 0))

## Remove data points with intensities below 10
res <- filterIntensity(chr1, 10)
intensity(res)

## Remove data points with an intensity lower than 10% of the maximum
## intensity in the Chromatogram
filt_fun <- function(x, prop = 0.1) {
    x@intensity >= max(x@intensity, na.rm = TRUE) * prop
}
res <- filterIntensity(chr1, filt_fun)
intensity(res)

## Remove data points with an intensity lower than half of the maximum
res <- filterIntensity(chr1, filt_fun, prop = 0.5)
intensity(res)

## log2 transform intensity values
res <- transformIntensity(chr1, log2)
intensity(res)
log2(intensity(chr1))

Description

The chromatogram method extracts chromatogram(s) from an MSnExp or OnDiskMSnExp object. Depending on the provided parameters this can be a total ion chromatogram (TIC), a base peak chromatogram (BPC) or an extracted ion chromatogram (XIC) extracted from each sample/file.

Usage

## S4 method for signature 'MSnExp'
chromatogram(
  object,
  rt,
  mz,
  aggregationFun = "sum",
  missing = NA_real_,
  msLevel = 1L,
  BPPARAM = bpparam()
)

Arguments

Details

Arguments rt and mz allow to specify the MS data slice from which the chromatogram should be extracted. The parameter aggregationSum allows to specify the function to be used to aggregate the intensities across the mz range for the same retention time. Setting aggregationFun = "sum" would e.g. allow to calculate the total ion chromatogram (TIC), aggregationFun = "max" the base peak chromatogram (BPC). The length of the extracted Chromatogram object, i.e. the number of available data points, corresponds to the number of scans/spectra measured in the specified retention time range. If in a specific scan (for a give retention time) no signal was measured in the specified mz range, a NA_real_ is reported as intensity for the retention time (see Notes for more information). This can be changed using the missing parameter.

By default or if \code{mz} and/or \code{rt} are numeric vectors, the
function extracts one \code{\link{Chromatogram}} object for each file
in the \code{\linkS4class{MSnExp}} or \code{\linkS4class{OnDiskMSnExp}}
object. Providing a numeric matrix with argument \code{mz} or \code{rt}
enables to extract multiple chromatograms per file, one for each row in
the matrix. If the number of columns of \code{mz} or \code{rt} are not
equal to 2, \code{range} is called on each row of the matrix.

Value

chromatogram returns a MChromatograms object with the number of columns corresponding to the number of files in object and number of rows the number of specified ranges (i.e. number of rows of matrices provided with arguments mz and/or rt). The featureData of the returned object contains columns "mzmin" and "mzmax" with the values from input argument mz (if used) and "rtmin" and "rtmax" if the input argument rt was used.

Author(s)

Johannes Rainer

See Also

Chromatogram and MChromatograms for the classes that represent single and multiple chromatograms.

Examples

## Read a test data file.
library(BiocParallel)
register(SerialParam())
library(msdata)
f <- c(system.file("microtofq/MM14.mzML", package = "msdata"),
     system.file("microtofq/MM8.mzML", package = "msdata"))

## Read the data as an MSnExp
msd <- readMSData(f, msLevel = 1)

## Extract the total ion chromatogram for each file:
tic <- chromatogram(msd)

tic

## Extract the TIC for the second file:
tic[1, 2]

## Plot the TIC for the first file
plot(rtime(tic[1, 1]), intensity(tic[1, 1]), type = "l",
    xlab = "rtime", ylab = "intensity", main = "TIC")

## Extract chromatograms for a MS data slices defined by retention time
## and mz ranges.
rtr <- rbind(c(10, 60), c(280, 300))
mzr <- rbind(c(140, 160), c(300, 320))
chrs <- chromatogram(msd, rt = rtr, mz = mzr)

## Each row of the returned MChromatograms object corresponds to one mz-rt
## range. The Chromatogram for the first range in the first file is empty,
## because the retention time range is outside of the file's rt range:
chrs[1, 1]

## The mz and/or rt ranges used are provided as featureData of the object
fData(chrs)

## The mz method can be used to extract the m/z ranges directly
mz(chrs)

## Also the Chromatogram for the second range in the second file is empty
chrs[2, 2]

## Get the extracted chromatogram for the first range in the second file
chr <- chrs[1, 2]
chr

plot(rtime(chr), intensity(chr), xlab = "rtime", ylab = "intensity")

Description

This method cleans out individual spectra (Spectrum instances), chromatograms (Chromatogram instances) or whole experiments (MSnExp instances) of 0-intensity peaks. Unless all is set to FALSE, original 0-intensity values are retained only around peaks. If more than two 0's were separating two peaks, only the first and last ones, those directly adjacent to the peak ranges are kept. If two peaks are separated by only one 0-intensity value, it is retained. An illustrative example is shown below.

Methods

signature(object = "MSnExp", all = "logical", verbose = "logical")

Cleans all spectra in MSnExp object. Displays a control bar if verbose set to TRUE (default). Returns a cleaned MSnExp instance.

signature(object = "Spectrum", all = "logical", msLevel. = "numeric")

Cleans the Spectrum object. Returns a cleaned Spectrum instance. If all = TRUE, then all zeros are removed. msLevel. defines the level of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

signature(object = "Chromatogram", all = "logical", na.rm = "logical")

Cleans the Chromatogram instance and returns a cleaned Chromatogram object. If na.rm is TRUE (default is FALSE) all NA intensities are removed before cleaning the chromatogram.

Author(s)

Laurent Gatto

See Also

removePeaks and trimMz for other spectra processing methods.

Examples

int <- c(1,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0)
sp1 <- new("Spectrum2",
           intensity=int,
           mz=1:length(int))
sp2 <- clean(sp1) ## default is all=FALSE
intensity(sp1)
intensity(sp2)
intensity(clean(sp1, all = TRUE))

mz(sp1)
mz(sp2)
mz(clean(sp1, all = TRUE))

data(itraqdata)
itraqdata2 <- clean(itraqdata)
sum(peaksCount(itraqdata))
sum(peaksCount(itraqdata2))
processingData(itraqdata2)

## Create a simple Chromatogram object
chr <- Chromatogram(rtime = 1:12,
                    intensity = c(0, 0, 20, 0, 0, 0, 123, 124343, 3432, 0, 0, 0))

## Remove 0-intensity values keeping those adjacent to peaks
chr <- clean(chr)
intensity(chr)

## Remove all 0-intensity values
chr <- clean(chr, all = TRUE)
intensity(chr)

## Clean a Chromatogram with NAs.
chr <- Chromatogram(rtime = 1:12,
                    intensity = c(0, 0, 20, NA, NA, 0, 123, 124343, 3432, 0, 0, 0))
chr <- clean(chr, all = FALSE, na.rm = TRUE)
intensity(chr)

Description

This function combines the features in an "MSnSet" instance applying a summarisation function (see fun argument) to sets of features as defined by a factor (see fcol argument). Note that the feature names are automatically updated based on the groupBy parameter.

The coefficient of variations are automatically computed and collated to the featureData slot. See cv and cv.norm arguments for details.

If NA values are present, a message will be shown. Details on how missing value impact on the data aggregation are provided below.

Arguments

Details

Missing values have different effect based on the aggregation method employed, as detailed below. See also examples below.

1. When using either "sum", "mean", "weighted.mean" or "median", any missing value will be propagated at the higher level. If na.rm = TRUE is used, then the missing value will be ignored.

2. Missing values will result in an error when using "medpolish", unless na.rm = TRUE is used.

3. When using robust summarisation ("robust"), individual missing values are excluded prior to fitting the linear model by robust regression. To remove all values in the feature containing the missing values, use filterNA.

4. The "iPQF" method will fail with an error if missing value are present, which will have to be handled explicitly. See below.

More generally, missing values often need dedicated handling such as filtering (see filterNA) or imputation (see impute).

Value

A new "MSnSet" instance is returned with ncol (i.e. number of samples) is unchanged, but nrow (i.e. the number od features) is now equals to the number of levels in groupBy. The feature metadata (featureData slot) is updated accordingly and only the first occurrence of a feature in the original feature meta-data is kept.

Author(s)

Laurent Gatto with contributions from Martina Fischer for iPQF and Ludger Goeminne, Adriaan Sticker and Lieven Clement for robust.

References

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Fischer M, Renard BY. Bioinformatics. 2016 Apr 1;32(7):1040-7. doi:10.1093/bioinformatics/btv675. Epub 2015 Nov 20. PubMed PMID:26589272.

See Also

featureCV to calculate coefficient of variation, nFeatures to document the number of features per group in the feature data, and the aggvar to explore variability within protein groups.

iPQF for iPQF summarisation.

NTR for normalisation to reference summarisation.

Examples

data(msnset)
msnset <- msnset[11:15, ]
exprs(msnset)

## arbitrary grouping into two groups
grp <- as.factor(c(1, 1, 2, 2, 2))
msnset.comb <- combineFeatures(msnset, groupBy = grp, method = "sum")
dim(msnset.comb)
exprs(msnset.comb)
fvarLabels(msnset.comb)

## grouping with a list
grpl <- list(c("A", "B"), "A", "A", "C", c("C", "B"))
## optional naming
names(grpl) <- featureNames(msnset)
exprs(combineFeatures(msnset, groupBy = grpl, method = "sum", redundancy.handler = "unique"))
exprs(combineFeatures(msnset, groupBy = grpl, method = "sum", redundancy.handler = "multiple"))

## missing data
exprs(msnset)[4, 4] <-
    exprs(msnset)[2, 2] <- NA
exprs(msnset)
## NAs propagate in the 115 and 117 channels
exprs(combineFeatures(msnset, grp, "sum"))
## NAs are removed before summing
exprs(combineFeatures(msnset, grp, "sum", na.rm = TRUE))

## using iPQF
data(msnset2)
anyNA(msnset2)
res <- combineFeatures(msnset2,
                       groupBy = fData(msnset2)$accession,
                       redundancy.handler = "unique",
                       method = "iPQF",
                       low.support.filter = FALSE,
                       ratio.calc = "sum",
                       method.combine = FALSE)
head(exprs(res))

## using robust summarisation
data(msnset) ## reset data
msnset <- log(msnset, 2) ## log2 transform

## Feature X46, in the ENO protein has one missig value
which(is.na(msnset), arr.ind = TRUE)
exprs(msnset["X46", ])
## Only the missing value in X46 and iTRAQ4.116 will be ignored
res <- combineFeatures(msnset,
                       fcol = "ProteinAccession",
                       method = "robust")
tail(exprs(res))

msnset2 <- filterNA(msnset) ## remove features with missing value(s)
res2 <- combineFeatures(msnset2,
                        fcol = "ProteinAccession",
                        method = "robust")
## Here, the values for ENO are different because the whole feature
## X46 that contained the missing value was removed prior to fitting.
tail(exprs(res2))

Description

combineSpectra combines spectra in a MSnExp, OnDiskMSnExp or MSpectra object applying the summarization function fun to sets of spectra defined by a factor (fcol parameter). The resulting combined spectrum for each set contains metadata information (present in mcols and all spectrum information other than mz and intensity) from the first spectrum in each set.

Combining of spectra for MSnExp or OnDiskMSnExp objects is performed by default for each file separately, combining of spectra across files is thus not possible. See examples for details.

Usage

## S4 method for signature 'MSnExp'
combineSpectra(
  object,
  fcol = "fileIdx",
  method = meanMzInts,
  ...,
  BPPARAM = bpparam()
)

## S4 method for signature 'MSpectra'
combineSpectra(object, fcol, method = meanMzInts, fun, ...)

Arguments

Value

A MSpectra or MSnExp object with combined spectra. Metadata (mcols) and all spectrum attributes other than mz and intensity are taken from the first Spectrum in each set.

Author(s)

Johannes Rainer, Laurent Gatto

See Also

meanMzInts() for a function to combine spectra.

Examples

set.seed(123)
mzs <- seq(1, 20, 0.1)
ints1 <- abs(rnorm(length(mzs), 10))
ints1[11:20] <- c(15, 30, 90, 200, 500, 300, 100, 70, 40, 20) # add peak
ints2 <- abs(rnorm(length(mzs), 10))
ints2[11:20] <- c(15, 30, 60, 120, 300, 200, 90, 60, 30, 23)
ints3 <- abs(rnorm(length(mzs), 10))
ints3[11:20] <- c(13, 20, 50, 100, 200, 100, 80, 40, 30, 20)

## Create the spectra.
sp1 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
    intensity = ints1, rt = 1)
sp2 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.01),
    intensity = ints2, rt = 2)
sp3 <- new("Spectrum1", mz = mzs + rnorm(length(mzs), sd = 0.009),
    intensity = ints3, rt = 3)

spctra <- MSpectra(sp1, sp2, sp3,
    elementMetadata = DataFrame(idx = 1:3, group = c("b", "a", "a")))

## Combine the spectra reporting the maximym signal
res <- combineSpectra(spctra, mzd = 0.05, intensityFun = max)
res

## All values other than m/z and intensity are kept from the first spectrum
rtime(res)

## Plot the individual and the merged spectrum
par(mfrow = c(2, 1), mar = c(4.3, 4, 1, 1))
plot(mz(sp1), intensity(sp1), xlim = range(mzs[5:25]), type = "h", col = "red")
points(mz(sp2), intensity(sp2), type = "h", col = "green")
points(mz(sp3), intensity(sp3), type = "h", col = "blue")
plot(mz(res[[1]]), intensity(res[[1]]), type = "h",
    col = "black", xlim = range(mzs[5:25]))

## Combine spectra in two sets.
res <- combineSpectra(spctra, fcol = "group", mzd = 0.05)
res

rtime(res)

## Plot the individual and the merged spectra
par(mfrow = c(3, 1), mar = c(4.3, 4, 1, 1))
plot(mz(sp1), intensity(sp1), xlim = range(mzs[5:25]), type = "h", col = "red")
points(mz(sp2), intensity(sp2), type = "h", col = "green")
points(mz(sp3), intensity(sp3), type = "h", col = "blue")
plot(mz(res[[1]]), intensity(res[[1]]), xlim = range(mzs[5:25]), type = "h",
    col = "black")
plot(mz(res[[2]]), intensity(res[[2]]), xlim = range(mzs[5:25]), type = "h",
    col = "black")

## Combining spectra of an MSnExp/OnDiskMSnExp objects
## Reading data from 2 mzML files
sciex <- readMSData(dir(system.file("sciex", package = "msdata"),
    full.names = TRUE), mode = "onDisk")

## Filter the file to a retention time range from 2 to 20 seconds (to reduce
## execution time of the example)
sciex <- filterRt(sciex, rt = c(2, 20))
table(fromFile(sciex))

## We have thus 64 spectra per file.

## In the example below we combine spectra measured in one second to a
## single spectrum. We thus first define the grouping variable and add that
## to the `fData` of the object. For combining, we use the
## `consensusSpectrum` function that combines the spectra keeping only peaks
## that were found in 50% of the spectra; by defining `mzd = 0.01` all peaks
## within an m/z of 0.01 are evaluated for combining.
seconds <- round(rtime(sciex))
head(seconds)
fData(sciex)$second <- seconds

res <- combineSpectra(sciex, fcol = "second", mzd = 0.01, minProp = 0.1,
    method = consensusSpectrum)
table(fromFile(res))

## The data was reduced to 19 spectra for each file.

Description

combineSpectraMovingWindow combines signal from consecutive spectra within a file. The resulting MSnExp has the same total number of spectra than the original object, but with each individual's spectrum information representing aggregated data from the original spectrum and its neighboring spectra. This is thus equivalent with a smoothing of the data in retention time dimension.

Note that the function returns always a MSnExp object, even if x was an OnDiskMSnExp object.

Usage

combineSpectraMovingWindow(
  x,
  halfWindowSize = 1L,
  intensityFun = base::mean,
  mzd = NULL,
  timeDomain = FALSE,
  weighted = FALSE,
  ppm = 0,
  BPPARAM = bpparam()
)

Arguments

Details

The method assumes same ions being measured in consecutive scans (i.e. LCMS data) and thus combines their signal which can increase the increase the signal to noise ratio.

Intensities (and m/z values) for signals with the same m/z value in consecutive scans are aggregated using the intensityFun. m/z values of intensities from consecutive scans will never be exactly identical, even if they represent signal from the same ion. The function determines thus internally a similarity threshold based on differences between m/z values within and between spectra below which m/z values are considered to derive from the same ion. For robustness reasons, this threshold is estimated on the 100 spectra with the largest number of m/z - intensity pairs (i.e. mass peaks).

See meanMzInts() for details.

Parameter timeDomain: by default, m/z-intensity pairs from consecutive scans to be aggregated are defined based on the square root of the m/z values. This is because it is highly likely that in all QTOF MS instruments data is collected based on a timing circuit (with a certain variance) and m/z values are later derived based on the relationship t = k * sqrt(m/z). Differences between individual m/z values will thus be dependent on the actual m/z value causing both the difference between m/z values and their scattering being different in the lower and upper m/z range. Determining m/z values to be combined on the sqrt(mz) reduces this dependency. For non-QTOF MS data timeDomain = FALSE might be used instead.

Value

MSnExp with the same number of spectra than x.

Note

The function has to read all data into memory for the spectra combining and thus the memory requirements of this function are high, possibly preventing its usage on large experimental data. In these cases it is suggested to perform the combination on a per-file basis and save the results using the writeMSData() function afterwards.

Author(s)

Johannes Rainer, Sigurdur Smarason

See Also

meanMzInts() for the function combining spectra provided in a list.

estimateMzScattering() for a function to estimate m/z value scattering in consecutive spectra.

Examples

library(MSnbase)
library(msdata)

## Read a profile-mode LC-MS data file.
fl <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)[1]
od <- readMSData(fl, mode = "onDisk")

## Subset the object to the retention time range that includes the signal
## for proline. This is done for performance reasons.
rtr <- c(165, 175)
od <- filterRt(od, rtr)

## Combine signal from neighboring spectra.
od_comb <- combineSpectraMovingWindow(od)

## The combined spectra have the same number of spectra, same number of
## mass peaks per spectra, but the signal is larger in the combined object.
length(od)
length(od_comb)

peaksCount(od)
peaksCount(od_comb)

## Comparing the chromatographic signal for proline (m/z ~ 116.0706)
## before and after spectra data combination.
mzr <- c(116.065, 116.075)
chr <- chromatogram(od, rt = rtr, mz = mzr)
chr_comb <- chromatogram(od_comb, rt = rtr, mz = mzr)

par(mfrow = c(1, 2))
plot(chr)
plot(chr_comb)
## Chromatographic data is "smoother" after combining.

Description

Subsets MSnSet instances to their common feature names.

Usage

commonFeatureNames(x, y)

Arguments

Value

An linkS4class{MSnSetList} composed of the input MSnSet containing only common features in the same order. The names of the output are either the names of the x and y input variables or the names of x if a list is provided.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(tan2009r1)
data(tan2009r2)
cmn <- commonFeatureNames(tan2009r1, tan2009r2)
names(cmn)
## as a named list
names(commonFeatureNames(list(a = tan2009r1, b = tan2009r2)))
## without message
suppressMessages(cmn <- commonFeatureNames(tan2009r1, tan2009r2))
## more than 2 instance
data(tan2009r3)
cmn <- commonFeatureNames(list(tan2009r1, tan2009r2, tan2009r3))
length(cmn)

Description

Compares two MSnSet instances. The qual and processingData slots are generally omitted.

Usage

compareMSnSets(x, y, qual = FALSE, proc = FALSE)

Arguments

Value

A logical

Author(s)

Laurent Gatto

Description

This method compares spectra (Spectrum instances) pairwise or all spectra of an experiment (MSnExp instances). Currently the comparison is based on the number of common peaks fun = "common", the Pearson correlation fun = "cor", the dot product fun = "dotproduct" or a user-defined function.

For fun = "common" the tolerance (default 25e-6) can be set and the tolerance can be defined to be relative (default relative = TRUE) or absolute (relative = FALSE). To compare spectra with fun = "cor" and fun = "dotproduct", the spectra need to be binned. The binSize argument (in Dalton) controls the binning precision. Please see bin for details.

Instead of these three predefined functions for fun a user-defined comparison function can be supplied. This function takes two Spectrum objects as the first two arguments and ... as third argument. The function must return a single numeric value. See the example section.

Methods

signature(x = "MSnExp", y = "missing", fun = "character", ...)

Compares all spectra in an MSnExp object. The ... arguments are passed to the internal functions. Returns a matrix of dimension length(x) by length(x).

signature(x = "Spectrum", y = "Spectrum", fun = "character", ...)

Compares two Spectrum objects. See the above explanation for fun and .... Returns a single numeric value.

Author(s)

Sebastian Gibb <[email protected]>

References

Stein, S. E., & Scott, D. R. (1994). Optimization and testing of mass spectral library search algorithms for compound identification. Journal of the American Society for Mass Spectrometry, 5(9), 859-866. doi: https://doi.org/10.1016/1044-0305(94)87009-8

Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E. and Aebersold, R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics, 7: 655-667. doi: https://doi.org/10.1002/pmic.200600625

See Also

bin, clean, pickPeaks, smooth, removePeaks and trimMz for other spectra processing methods.

Examples

s1 <- new("Spectrum2", mz=1:10, intensity=1:10)
s2 <- new("Spectrum2", mz=1:10, intensity=10:1)
compareSpectra(s1, s2)
compareSpectra(s1, s2, fun="cor", binSize=2)
compareSpectra(s1, s2, fun="dotproduct")

## define our own (useless) comparison function (it is just a basic example)
equalLength <- function(x, y, ...) {
  return(peaksCount(x)/(peaksCount(y)+.Machine$double.eps))
}
compareSpectra(s1, s2, fun=equalLength)
compareSpectra(s1, new("Spectrum2", mz=1:5, intensity=1:5), fun=equalLength)
compareSpectra(s1, new("Spectrum2"), fun=equalLength)

data(itraqdata)
compareSpectra(itraqdata[1:5], fun="cor")

Description

consensusSpectrum takes a list of spectra and combines them to a consensus spectrum containing mass peaks that are present in a user definable proportion of spectra.

Usage

consensusSpectrum(
  x,
  mzd = 0,
  minProp = 0.5,
  intensityFun = stats::median,
  mzFun = stats::median,
  ppm = 0,
  weighted = FALSE,
  ...
)

Arguments

Details

Peaks from spectra with a difference of their m/z being smaller than mzd are grouped into the same final mass peak with their intensities being aggregated with intensityFun. Alternatively (or in addition) it is possible to perform an m/z dependent grouping of mass peaks with parameter ppm: mass peaks from different spectra with a difference in their m/z smaller than ppm of their m/z are grouped into the same final peak.

The m/z of the final mass peaks is calculated with mzFun. By setting weighted = TRUE the parameter mzFun is ignored and an intensity-weighted mean of the m/z values from the individual mass peaks is returned as the peak's m/z.

Author(s)

Johannes Rainer

See Also

Other spectra combination functions: meanMzInts()

Examples

library(MSnbase)
## Create 3 example spectra.
sp1 <- new("Spectrum2", rt = 1, precursorMz = 1.41,
    mz = c(1.2, 1.5, 1.8, 3.6, 4.9, 5.0, 7.8, 8.4),
    intensity = c(10, 3, 140, 14, 299, 12, 49, 20))
sp2 <- new("Spectrum2", rt = 1.1, precursorMz = 1.4102,
    mz = c(1.4, 1.81, 2.4, 4.91, 6.0, 7.2, 9),
    intensity = c(3, 184, 8, 156, 12, 23, 10))
sp3 <- new("Spectrum2", rt = 1.2, precursorMz = 1.409,
    mz = c(1, 1.82, 2.2, 3, 7.0, 8),
    intensity = c(8, 210, 7, 101, 17, 8))
spl <- MSpectra(sp1, sp2, sp3)

## Plot the spectra, each in a different color
par(mfrow = c(2, 1), mar = c(4.3, 4, 1, 1))
plot(mz(sp1), intensity(sp1), type = "h", col = "#ff000080", lwd = 2,
    xlab = "m/z", ylab = "intensity", xlim = range(mz(spl)),
    ylim = range(intensity(spl)))
points(mz(sp2), intensity(sp2), type = "h", col = "#00ff0080", lwd = 2)
points(mz(sp3), intensity(sp3), type = "h", col = "#0000ff80", lwd = 2)

cons <- consensusSpectrum(spl, mzd = 0.02, minProp = 2/3)

## Peaks of the consensus spectrum
mz(cons)
intensity(cons)

## Other Spectrum data is taken from the first Spectrum in the list
rtime(cons)
precursorMz(cons)

plot(mz(cons), intensity(cons), type = "h", xlab = "m/z", ylab = "intensity",
    xlim = range(mz(spl)), ylim = range(intensity(spl)), lwd = 2)

Description

estimateMzResolution estimates the m/z resolution of a profile-mode Spectrum (or of all spectra in an MSnExp or OnDiskMSnExp object. The m/z resolution is defined as the most frequent difference between a spectrum's m/z values.

Usage

## S4 method for signature 'MSnExp'
estimateMzResolution(object, ...)

## S4 method for signature 'Spectrum'
estimateMzResolution(object, ...)

Arguments

Value

numeric(1) with the m/z resolution. If called on a MSnExp or OnDiskMSnExp a list of m/z resolutions are returned (one for each spectrum).

Note

This assumes the data to be in profile mode and does not return meaningful results for centroided data.

The estimated m/z resolution depends on the number of ions detected in a spectrum, as some instrument don't measure (or report) signal if below a certain threshold.

Author(s)

Johannes Rainer

Examples

## Load a profile mode example file
library(BiocParallel)
register(SerialParam())
library(msdata)
f <- proteomics(full.names = TRUE,
    pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")

od <- readMSData(f, mode = "onDisk")

## Estimate the m/z resolution on the 3rd spectrum.
estimateMzResolution(od[[3]])

## Estimate the m/z resolution for each spectrum
mzr <- estimateMzResolution(od)

## plot the distribution of estimated m/z resolutions. The bimodal
## distribution represents the m/z resolution of the MS1 (first peak) and
## MS2 spectra (second peak).
plot(density(unlist(mzr)))

Description

Estimate scattering of m/z values (due to technical, instrument specific noise) for the same ion in consecutive scans of a LCMS experiment.

Usage

estimateMzScattering(x, halfWindowSize = 1L, timeDomain = FALSE)

Arguments

Details

The m/z values of the same ions in consecutive scans (spectra) of a LCMS run will not be identical. This random noise is expected to be smaller than the resolution of the MS instrument. The distribution of differences of m/z values from neighboring spectra is thus expected to be (at least) bi-modal with the first peak representing the above described random variation and the second (or largest) peak the m/z resolution. The m/z value of the first local minimum between these first two peaks in the distribution is returned as the m/z scattering.

Note

For timeDomain = TRUE the function does not return the estimated scattering of m/z values, but the scattering of sqrt(mz) values.

Author(s)

Johannes Rainer

See Also

estimateMzResolution() for the function to estimate a profile-mode spectrum's m/z resolution from it's data.

Examples

library(MSnbase)
library(msdata)
## Load a profile-mode LC-MS data file
f <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)[1]
od <- readMSData(f, mode = "onDisk")
im <- as(filterRt(od, c(10, 20)), "MSnExp")

res <- estimateMzScattering(im)

## Plot the distribution of estimated m/z scattering
plot(density(unlist(res)))

## Compare the m/z resolution and m/z scattering of the spectrum with the
## most peaks
idx <- which.max(unlist(spectrapply(im, peaksCount)))

res[[idx]]
abline(v = res[[idx]], lty = 2)
estimateMzResolution(im[[idx]])
## As expected, the m/z scattering is much lower than the m/z resolution.

Description

This method performs a noise estimation on individual spectra (Spectrum instances). There are currently two different noise estimators, the Median Absolute Deviation (method = "MAD") and Friedman's Super Smoother (method = "SuperSmoother"), as implemented in the MALDIquant::detectPeaks and MALDIquant::estimateNoise functions respectively.

Methods

signature(object = "Spectrum", method = "character", ...)

Estiamtes the noise in a non-centroided spectrum (Spectrum instance). method could be "MAD" or "SuperSmoother". The arguments ... are passed to the noise estimator functions implemented in MALDIquant::estimateNoise. Currenlty only the method = "SuperSmoother" accepts additional arguments, e.g. span. Please see supsmu for details. This method returns a two-column matrix with the m/z and intensity values in the first and the second column.

signature(object = "MSnExp", method = "character", ...)

Estimates noise for all spectra in object.

Author(s)

Sebastian Gibb <[email protected]>

References

S. Gibb and K. Strimmer. 2012. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/

See Also

pickPeaks, and the underlying method in MALDIquant: estimateNoise.

Examples

sp1 <- new("Spectrum1",
           intensity = c(1:6, 5:1),
           mz = 1:11,
           centroided = FALSE)
estimateNoise(sp1, method = "SuperSmoother")

Description

The expandFeatureVars and mergeFeatureVars respectively expand and merge groups of feature variables. Using these functions, a set of columns in a feature data can be merged into a single new data.frame-column variables and a data.frame-column can be expanded into single feature columns. The original feature variables are removed.

Usage

expandFeatureVars(x, fcol, prefix)

mergeFeatureVars(x, fcol, fcol2)

Arguments

Value

An MSnSet for expanded (merged) feature variables.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(hyperLOPIT2015)
fvarLabels(hyperLOPIT2015)
## Let's merge all svm prediction feature variables
(k <- grep("^svm", fvarLabels(hyperLOPIT2015), value = TRUE))
hl <- mergeFeatureVars(hyperLOPIT2015, fcol = k, fcol2 = "SVM")
fvarLabels(hl)
head(fData(hl)$SVM)

## Let's expand the new SVM into individual columns
hl2 <- expandFeatureVars(hl, "SVM")
fvarLabels(hl2)
## We can set the prefix manually
hl2 <- expandFeatureVars(hl, "SVM", prefix = "Expanded")
fvarLabels(hl2)
## If we don't want any prefix
hl2 <- expandFeatureVars(hl, "SVM", prefix = NULL)
fvarLabels(hl2)

Description

Extracts the MSMS spectra that originate from the precursor(s) having the same MZ value as defined in theprec argument.

A warning will be issued of one or several of the precursor MZ values in prec are absent in the experiment precursor MZ values (i.e in precursorMz(object)).

Methods

signature(object = "MSnExp", prec = "numeric")

Returns an "MSnExp" containing MSMS spectra whose precursor MZ values are in prec.

Author(s)

Laurent Gatto

Examples

file <- dir(system.file(package="MSnbase",dir="extdata"),
            full.name=TRUE,pattern="mzXML$")
aa <- readMSData(file,verbose=FALSE)
my.prec <- precursorMz(aa)[1]
my.prec
bb <- extractPrecSpectra(aa,my.prec)
precursorMz(bb)
processingData(bb)

Description

The Spectra package provides a more robust and efficient infrastructure for mass spectrometry data handling and analysis. So, wherever possible, the newer Spectra package should be used instead of the MSnbase. The functions listed here allow to convert between objects from the MSnbase and Spectra packages.

extractSpectraData extracts the spectra data (m/z and intensity values including metadata) from MSnExp, OnDiskMSnExp, Spectrum1, Spectrum2 objects (or list of such objects) and returns these as a DataFrame that can be used to create a Spectra::Spectra object.This function enables thus to convert data from the old MSnbase package to the newer Spectra package.

To convert a Spectra object to a MSpectra object use as(sps, "MSpectra") where sps is a Spectra object.

Usage

extractSpectraData(x)

Arguments

Value

• extracSpectraData() returns a DataFrame() with the full spectrum data that can be passed to the Spectra::Spectra() function to create a Spectra object.

• as(x, "MSpectra") returns a MSpectra object with the content of the Spectra object x.

Note

Coercion from Spectra to a MSpectra will only assign values to the contained Spectrum1 and Spectrum2 objects, but will not add all eventually spectra variables present in Spectra.

Author(s)

Johannes Rainer

Examples

## Read an mzML file with MSnbase
fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
    package = "msdata")
data <- filterRt(readMSData(fl, mode = "onDisk"), rt = c(1, 6))

## Extract the data as a DataFrame
res <- extractSpectraData(data)
res

library(Spectra)
## This can be used as an input for the Spectra constructor of the
## Spectra package:
sps <- Spectra::Spectra(res)
sps

## A Spectra object can be coerced to a MSnbase MSpectra object using
msps <- as(sps, "MSpectra")

Description

This function produces the opposite as the stringsAsFactors argument in the data.frame or read.table functions; it converts factors columns to characters.

Usage

factorsAsStrings(x)

Arguments

Value

A data.frame where factors are converted to characters.

Author(s)

Laurent Gatto

Examples

data(iris)
str(iris)
str(factorsAsStrings(iris))

Description

Comparing feature names of two comparable MSnSet instances.

Objects from the Class

Objects can be created with compfnames. The method compares the feature names of two objects of class "MSnSet". It prints a summary matrix of common and unique feature names and invisibly returns a list of FeatComp instances.

The function will compute the common and unique features for all feature names of the two input objects (featureNames(x) and feautreNames(y)) as well as distinct subsets as defined in the fcol1 and fcol2 feautre variables.

Slots

name:

Object of class "character" defining the name of the compared features. By convention, "all" is used when all feature names are used; otherwise, the respective levels of the feature variables fcol1 and fcol2.

common:

Object of class "character" with the common feature names.

unique1:

Object of class "character" with the features unique to the first MSnSet (x in compfname).

unique2:

Object of class "character" with the features unique to the seconn MSnSet (y in compfname).

all:

Object of class "logical" defining if all features of only a subset were compared. One expects that name == "all" when all is TRUE.

Methods

Accessors names, common, unique1 and unique2 can be used to access the respective FeatComp slots.

compfnames

signature(x = "MSnSet", y = "MSnSet", fcol1 = "character", fcol2 = "character", simplify = "logical", verbose = "logical"): creates the FeatComp comparison object for instances x and y. The feature variables to be considered to details feature comparison can be defined by fcol1 (default is "markers" and fcol2 for x and y respectively). Setting either to NULL will only consider all feature names; in such case, of simplify is TRUE (default), an FeatComp object is returned instead of a list of length 1. The verbose logical controls if a summary table needs to be printed (default is TRUE).

compfnames

signature(x = "list", y = "missing", ...): when x is a list of MSnSet instances, compfnames is applied to all element pairs of x. Additional parameters fcol1, fcol2, simplify and verbose are passed to the pairwise comparison method.

show

signature(object = "FeatComp"): prints a summary of the object.

Author(s)

Laurent Gatto and Thomas Naake

See Also

averageMSnSet to compuate an average MSnSet.

Examples

library("pRolocdata")
data(tan2009r1)
data(tan2009r2)
x <- compfnames(tan2009r1, tan2009r2)
x[[1]]
x[2:3]
head(common(x[[1]]))

data(tan2009r3)
tanl <- list(tan2009r1, tan2009r2, tan2009r3)
xx <- compfnames(tanl, fcol1 = NULL)
length(xx)
tail(xx)

all.equal(xx[[15]],
          compfnames(tan2009r2, tan2009r3, fcol1 = NULL))
str(sapply(xx, common))

Description

This function calculates the column-wise coefficient of variation (CV), i.e. the ration between the standard deviation and the mean, for the features in an MSnSet. The CVs are calculated for the groups of features defined by groupBy. For groups defined by single features, NA is returned.

Usage

featureCV(x, groupBy, na.rm = TRUE, norm = "none", suffix = NULL)

Arguments

Value

A matrix of dimensions length(levels(groupBy)) by ncol(x) with the respecive CVs. The column names are formed by pasting CV. and the sample names of object x, possibly suffixed by .suffix.

Author(s)

Laurent Gatto and Sebastian Gibb

See Also

combineFeatures()

Examples

data(msnset)
msnset <- msnset[1:4]
gb <- factor(rep(1:2, each = 2))
featureCV(msnset, gb)
featureCV(msnset, gb, suffix = "2")

Description

The Features of Interest infrastructure allows to define a set of features of particular interest to be used/matched against existing data sets contained in "MSnSet". A specific set of features is stored as an FeaturesOfInterest object and a collection of such non-redundant instances (for example for a specific organism, project, ...) can be collected in a FoICollection.

Objects from the Class

Objects can be created with the respective FeaturesOfInterest and FoICollection constructors.

FeaturesOfInterest instances can be generated in two different ways: the constructor takes either (1) a set of features names (a character vector) and a description (character of length 1 - any subsequent elements are silently ignored) or (2) feature names, a description and an instance of class "MSnSet". In the latter case, we call such FeaturesOfInterest objects traceable, because we can identify the origin of the feature names and thus their validity. This is done by inspecting the MSnSet instance and recording its dimensions, its name and a unique md5 hash tag (these are stores as part of the optional objpar slot). In such cases, the feature names passed to the FeaturesOfInterest constructor must also be present in the MSnSet; if one or more are not, an error will be thrown. If your features of interest to be recorded stem for an existing experiment and have all been observed, it is advised to pass the 3 arguments to the constructor to ensure that the feature names as valid. Otherwise, only the third argument should be omitted.

FoICollection instances can be constructed by creating an empty collection and serial additions of FeaturesOfInterest using addFeaturesOfInterest or by passing a list of FeaturesOfInterest instance.

Slots

FeaturesOfInterest class:

description:

Object of class "character" describing the instance.

objpar:

Optional object of class "list" providing details about the MSnSet instance originally used to create the instance. See details section.

fnames:

Object of class "character" with the feature of interest names.

date:

Object of class "character" with the date the instance was first generated.

.__classVersion__:

Object of class "Versions" with the FeaturesOfInterest class version. Only relevant for development.

FoICollection class:

foic:

Object of class "list" with the FeaturesOfInterest.

.__classVersion__:

Object of class "Versions" with the FoICollection class version. Only relevant for development.

Extends

Class "Versioned", directly.

Methods

FeaturesOfInterest class:

description

signature(object = "FeaturesOfInterest"): returns the description of object.

foi

signature(object = "FeaturesOfInterest"): returns the features of interests.

length

signature(x = "FeaturesOfInterest"): returns the number of features of interest in x.

show

signature(object = "FeaturesOfInterest"): displays object.

fnamesIn

signature(x = "FeaturesOfInterst", y = "MSnSet", count = "logical"): if count is FALSE (default), return a logical indicating whether there is at least one feautre of interest present in x? Otherwise, returns the number of such features. Works also with matrices and data.frames.

[

Subsetting works like lists. Returns a new FoICollection.

[[

Subsetting works like lists. Returns a new FeatureOfInterest.

FoICollection class:

description

signature(object = "FoICollection"): returns the description of object.

foi

signature(object = "FoICollection"): returns a list of FeaturesOfInterest.

length

signature(x = "FoICollection"): returns the number of FeaturesOfInterest in the collection.

lengths

signature(x = "FoICollection"): returns the number of features of interest in each FeaturesOfInterest in the collection x.

addFeaturesOfInterest

signature(x = "FeaturesOfInterest", y = "FoICollection"): add the FeaturesOfInterest instance x to FoICollection y. If x is already present, a message is printed and y is returned unchanged.

rmFeaturesOfInterest

signature(object = "FoICollection", i = "numeric"): removes the ith FeatureOfInterest in the collection object.

show

signature(object = "FoICollection"): displays object.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(tan2009r1)

x <- FeaturesOfInterest(description = "A traceable test set of features of interest",
                        fnames = featureNames(tan2009r1)[1:10],
                        object = tan2009r1)
x

description(x)
foi(x)

y <- FeaturesOfInterest(description = "Non-traceable features of interest",
                        fnames = featureNames(tan2009r1)[111:113])
y

## an illegal FeaturesOfInterest
try(FeaturesOfInterest(description = "Won't work",
                       fnames = c("A", "Z", featureNames(tan2009r1)),
                       object = tan2009r1))


FeaturesOfInterest(description = "This work, but not traceable",
                       fnames = c("A", "Z", featureNames(tan2009r1)))



xx <- FoICollection()
xx

xx <- addFeaturesOfInterest(x, xx)
xx <- addFeaturesOfInterest(y, xx)
names(xx) <- LETTERS[1:2]
xx

## Sub-setting
xx[1]
xx[[1]]
xx[["A"]]

description(xx)
foi(xx)

fnamesIn(x, tan2009r1)
fnamesIn(x, tan2009r1, count = TRUE)

rmFeaturesOfInterest(xx, 1)

Description

This function replaces all the empty characters "" and/or NAs with the value of the closest preceding the preceding non-NA/"" element. The function is used to populate dataframe or matrice columns where only the cells of the first row in a set of partially identical rows are explicitly populated and the following are empty.

Usage

fillUp(x)

Arguments

Value

A vector as x with all empty characters "" and NA values replaced by the preceding non-NA/"" value.

Author(s)

Laurent Gatto

Examples

d <- data.frame(protein=c("Prot1","","","Prot2","",""),
                peptide=c("pep11","","pep12","pep21","pep22",""),
                score=c(1:2,NA,1:3))
d
e <- apply(d,2,fillUp)
e
data.frame(e)
fillUp(d[,1])

Description

A function to filter out PSMs matching to the decoy database, of rank greater than one and matching non-proteotypic peptides.

Usage

filterIdentificationDataFrame(
  x,
  decoy = "isDecoy",
  rank = "rank",
  accession = "DatabaseAccess",
  spectrumID = "spectrumID",
  verbose = isMSnbaseVerbose()
)

Arguments

Details

The PSMs should be stored in a data.frame such as those produced by readMzIdData(). Note that this function should be called before calling the reduce method on a PSM data.frame.

Value

A new data.frame with filtered out peptides and with the same columns as the input x.

Author(s)

Laurent Gatto

Description

This function is used to convert retention times. Conversion is seconds to/from the more human friendly format "mm:sec". The implementation is from MsCoreUtils::formatRt().

Usage

formatRt(rt)

Arguments

Value

A vector of same length as rt.

Author(s)

Laurent Gatto and Sebastian Gibb

Examples

formatRt(1524)
formatRt("25:24")

Description

Return the name of variable varname in call match_call.

Usage

getVariableName(match_call, varname)

Arguments

Value

A character with the name of the variable passed as parameter varname in parent close of match_call.

Author(s)

Laurent Gatto

Examples

a <- 1
f <- function(x, y)
 MSnbase:::getVariableName(match.call(), "x")
f(x = a)
f(y = a)

Description

Given a text spread sheet f and a pattern to be matched to its header (first line in the file), the function returns the matching columns names or indices of the corresponding data.frame.

The function starts by reading the first line of the file (or connection) f with readLines, then splits it according to the optional ... arguments (it is important to correctly specify strsplit's split character vector here) and then matches pattern to the individual column names using grep.

Similarly, getEcols can be used to explore the column names and decide for the appropriate pattern value.

These functions are useful to check the parameters to be provided to readMSnSet2.

Usage

grepEcols(f, pattern, ..., n = 1)

getEcols(f, ..., n = 1)

Arguments

Value

Depending on value, the matching column names of indices. In case of getEcols, a character of column names.

Author(s)

Laurent Gatto

See Also

readMSnSet2

Description

Helper functions to check whether raw files contain spectra or chromatograms.

Usage

hasSpectra(files)

hasChromatograms(files)

Arguments

Value

A logical(n) where n == length(x) with TRUE if that files contains at least one spectrum, FALSE otherwise.

Author(s)

Laurent Gatto

Examples

f <- msdata::proteomics(full.names = TRUE)[1:2]
hasSpectra(f)
hasChromatograms(f)

Description

Produces a heatmap after reordring rows and columsn to highlight missing value patterns.

Usage

imageNA2(
  object,
  pcol,
  Rowv,
  Colv = TRUE,
  useGroupMean = FALSE,
  plot = TRUE,
  ...
)

Arguments

Value

Used for its side effect of plotting. Invisibly returns Rovw and Colv.

Author(s)

Laurent Gatto, Samuel Wieczorek and Thomas Burger

Examples

library("pRolocdata")
library("pRoloc")
data(dunkley2006)
pcol <- ifelse(dunkley2006$fraction <= 5, "A", "B")
nax <- makeNaData(dunkley2006, pNA = 0.10)
exprs(nax)[sample(nrow(nax), 30), pcol == "A"] <- NA
exprs(nax)[sample(nrow(nax), 50), pcol == "B"] <- NA
MSnbase:::imageNA2(nax, pcol)
MSnbase:::imageNA2(nax, pcol, useGroupMean = TRUE)
MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = FALSE)
MSnbase:::imageNA2(nax, pcol, Colv = FALSE, useGroupMean = TRUE)

Description

The impute method performs data imputation on MSnSet instances using a variety of methods.

Users should proceed with care when imputing data and take precautions to assure that the imputation produce valid results, in particular with naive imputations such as replacing missing values with 0.

See MsCoreUtils::impute_matrix() for details on the different imputation methods available and strategies.

Usage

## S4 method for signature 'MSnSet'
impute(object, method, ...)

Arguments

Examples

data(naset)

## table of missing values along the rows
table(fData(naset)$nNA)

## table of missing values along the columns
pData(naset)$nNA

## non-random missing values
notna <- which(!fData(naset)$randna)
length(notna)
notna

impute(naset, method = "min")

if (require("imputeLCMD")) {
    impute(naset, method = "QRILC")
    impute(naset, method = "MinDet")
}

if (require("norm"))
    impute(naset, method = "MLE")

impute(naset, "mixed",
       randna = fData(naset)$randna,
       mar = "knn", mnar = "QRILC")


## neighbour averaging
x <- naset[1:4, 1:6]

exprs(x)[1, 1] <- NA ## min value
exprs(x)[2, 3] <- NA ## average
exprs(x)[3, 1:2] <- NA ## min value and average
## 4th row: no imputation
exprs(x)

exprs(impute(x, "nbavg"))

Description

The iPQF spectra-to-protein summarisation method integrates peptide spectra characteristics and quantitative values for protein quantitation estimation. Spectra features, such as charge state, sequence length, identification score and others, contain valuable information concerning quantification accuracy. The iPQF algorithm assigns weights to spectra according to their overall feature reliability and computes a weighted mean to estimate protein quantities. See also combineFeatures for a more general overview of feature aggregation and examples.

Usage

iPQF(
  object,
  groupBy,
  low.support.filter = FALSE,
  ratio.calc = "sum",
  method.combine = FALSE,
  feature.weight = c(7, 6, 4, 3, 2, 1, 5)^2
)

Arguments

Value

A matrix with estimated protein ratios.

Author(s)

Martina Fischer

References

iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. Fischer M, Renard BY. Bioinformatics. 2016 Apr 1;32(7):1040-7. doi:10.1093/bioinformatics/btv675. Epub 2015 Nov 20. PubMed PMID:26589272.

Examples

data(msnset2)
head(exprs(msnset2))
prot <- combineFeatures(msnset2,
                        groupBy = fData(msnset2)$accession,
                        method = "iPQF")
head(exprs(prot))

Description

The function extracts the mode (profile or centroided) from the raw mass spectrometry file by parsing the mzML file directly. If the object x stems from any other type of file, NAs are returned.

Usage

isCentroidedFromFile(x)

Arguments

Details

This function is much faster than isCentroided(), which estimates mode from the data, but is limited to data stemming from mzML files which are still available in their original location (and accessed with fileNames(x)).

Value

A named logical vector of the same length as x.

Author(s)

Laurent Gatto

Examples

library("msdata")
f <- proteomics(full.names = TRUE,
                pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
x <- readMSData(f, mode = "onDisk")
table(isCentroidedFromFile(x), msLevel(x))

Description

This instance of class "ReporterIons" corresponds to the iTRAQ 4-plex set, i.e the 114, 115, 116 and 117 isobaric tags. In the iTRAQ5 data set, an unfragmented tag, i.e reporter and attached isobaric tag, is also included at MZ 145. These objects are used to plot the reporter ions of interest in an MSMS spectra (see "Spectrum2") as well as for quantification (see quantify).

Usage

iTRAQ4
iTRAQ5
iTRAQ8
iTRAQ9

References

Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. "Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents." Mol Cell Proteomics, 2004 Dec;3(12):1154-69. Epub 2004 Sep 22. PubMed PMID: 15385600.

See Also

TMT6.

Examples

iTRAQ4
iTRAQ4[1:2]

newReporter <- new("ReporterIons",
                   description="an example",
                   name="my reporter ions",
                   reporterNames=c("myrep1","myrep2"),
                   mz=c(121,122),
                   col=c("red","blue"),
                   width=0.05)
newReporter

Description

itraqdata is and example data sets is an iTRAQ 4-plex experiment that has been run on an Orbitrap Velos instrument. It includes identification data in the feature data slot obtain from the Mascot search engine. It is a subset of an spike-in experiment where proteins have spiked in an Erwinia background, as described in

Karp et al. (2010), Addressing accuracy and precision issues in iTRAQ quantitation, Mol Cell Proteomics. 2010 Sep;9(9):1885-97. Epub 2010 Apr 10. (PMID 20382981).

The spiked-in proteins in itradata are BSA and ENO and are present in relative abundances 1, 2.5, 5, 10 and 10, 5, 2.5, 1 in the 114, 115, 116 and 117 reporter tags.

The msnset object is produced by running the quantify method on the itraqdata experimental data, as detailed in the quantify example. This example data set is used in the MSnbase-demo vignette, available with vignette("MSnbase-demo", package="MSnbase").

The msnset2 object is another example iTRAQ4 data that is used to demonstrate features of the package, in particular the iPQF feature aggregation method, described in iPQF. It corresponds to 11 proteins with spectra measurements from the original data set described by Breitwieser et al. (2011) General statistical modeling of data from protein relative expression isobaric tags. J. Proteome Res., 10, 2758-2766.

Usage

itraqdata

Examples

data(itraqdata)
itraqdata

## created by
## msnset <- quantify(itraqdata, method = "trap", reporters = iTRAQ4)
data(msnset)
msnset

data(msnset2)
msnset2

Description

Compares equality of all members of a list.

Usage

listOf(x, class, valid = TRUE)

Arguments

Value

TRUE is all elements of x inherit from class.

Author(s)

Laurent Gatto

Examples

listOf(list(), "foo")
listOf(list("a", "b"), "character")
listOf(list("a", 1), "character")

Description

Convert a vector of characters to camel case by replacing dots by captial letters.

Usage

makeCamelCase(x, prefix)

Arguments

Value

A character of same length as x.

Author(s)

Laurent Gatto

Examples

nms <- c("aa.foo", "ab.bar")
makeCamelCase(nms)
makeCamelCase(nms, prefix = "x")

Description

These functions take an instance of class "MSnSet" and sets randomly selected values to NA.

Usage

makeNaData(object, nNA, pNA, exclude)

makeNaData2(object, nRows, nNAs, exclude)

whichNA(x)

Arguments

Details

makeNaData randomly selects a number nNA (or a proportion pNA) of cells in the expression matrix to be set to NA.

makeNaData2 will select length(nRows) sets of rows from object, each with nRows[i] rows respectively. The first set will be assigned nNAs[1] missing values, the second nNAs[2], ... As opposed to makeNaData, this permits to control the number of NAs per rows.

The whichNA can be used to extract the indices of the missing values, as illustrated in the example.

Value

An instance of class MSnSet, as object, but with the appropriate number/proportion of missing values. The returned object has an additional feature meta-data columns, nNA

Author(s)

Laurent Gatto

Examples

## Example 1
library(pRolocdata)
data(dunkley2006)
sum(is.na(dunkley2006))
dunkleyNA <- makeNaData(dunkley2006, nNA = 150)
processingData(dunkleyNA)
sum(is.na(dunkleyNA))
table(fData(dunkleyNA)$nNA)
naIdx <- whichNA(dunkleyNA)
head(naIdx)
## Example 2
dunkleyNA <- makeNaData(dunkley2006, nNA = 150, exclude = 1:10)
processingData(dunkleyNA)
table(fData(dunkleyNA)$nNA[1:10])
table(fData(dunkleyNA)$nNA)
## Example 3
nr <- rep(10, 5)
na <- 1:5
x <- makeNaData2(dunkley2006[1:100, 1:5],
                 nRows = nr,
                 nNAs = na)
processingData(x)
(res <- table(fData(x)$nNA))
stopifnot(as.numeric(names(res)[-1]) ==  na)
stopifnot(res[-1] ==  nr)
## Example 3
nr2 <- c(5, 12, 11, 8)
na2 <- c(3, 8, 1, 4)
x2 <- makeNaData2(dunkley2006[1:100, 1:10],
                  nRows = nr2,
                  nNAs = na2)
processingData(x2)
(res2 <- table(fData(x2)$nNA))
stopifnot(as.numeric(names(res2)[-1]) ==  sort(na2))
stopifnot(res2[-1] ==  nr2[order(na2)])
## Example 5
nr3 <- c(5, 12, 11, 8)
na3 <- c(3, 8, 1, 3)
x3 <- makeNaData2(dunkley2006[1:100, 1:10],
                  nRows = nr3,
                  nNAs = na3)
processingData(x3)
(res3 <- table(fData(x3)$nNA))

Description

The MChromatograms class allows to store Chromatogram() objects in a matrix-like two-dimensional structure.

Usage

MChromatograms(data, phenoData, featureData, ...)

## S4 method for signature 'MChromatograms'
show(object)

## S4 method for signature 'MChromatograms,ANY,ANY,ANY'
x[i, j, drop = FALSE]

## S4 replacement method for signature 'MChromatograms,ANY,ANY,ANY'
x[i, j] <- value

## S4 method for signature 'MChromatograms,ANY'
plot(
  x,
  col = "#00000060",
  lty = 1,
  type = "l",
  xlab = "retention time",
  ylab = "intensity",
  main = NULL,
  ...
)

## S4 method for signature 'MChromatograms'
phenoData(object)

## S4 method for signature 'MChromatograms'
pData(object)

## S4 replacement method for signature 'MChromatograms,data.frame'
pData(object) <- value

## S4 method for signature 'MChromatograms'
x$name

## S4 replacement method for signature 'MChromatograms'
x$name <- value

## S4 replacement method for signature 'MChromatograms,ANY'
colnames(x) <- value

## S4 method for signature 'MChromatograms'
sampleNames(object)

## S4 replacement method for signature 'MChromatograms,ANY'
sampleNames(object) <- value

## S4 method for signature 'MChromatograms'
isEmpty(x)

## S4 method for signature 'MChromatograms'
featureNames(object)

## S4 replacement method for signature 'MChromatograms'
featureNames(object) <- value

## S4 method for signature 'MChromatograms'
featureData(object)

## S4 replacement method for signature 'MChromatograms,ANY'
featureData(object) <- value

## S4 method for signature 'MChromatograms'
fData(object)

## S4 replacement method for signature 'MChromatograms,ANY'
fData(object) <- value

## S4 method for signature 'MChromatograms'
fvarLabels(object)

## S4 replacement method for signature 'MChromatograms'
rownames(x) <- value

## S4 method for signature 'MChromatograms'
precursorMz(object)

## S4 method for signature 'MChromatograms'
productMz(object)

## S4 method for signature 'MChromatograms'
mz(object)

## S4 method for signature 'MChromatograms'
polarity(object)

## S4 method for signature 'MChromatograms'
bin(x, binSize = 0.5, breaks = numeric(), fun = max)

## S4 method for signature 'MChromatograms'
clean(object, all = FALSE, na.rm = FALSE)

## S4 method for signature 'MChromatograms'
normalize(object, method = c("max", "sum"))

## S4 method for signature 'MChromatograms'
filterIntensity(object, intensity = 0, ...)

## S4 method for signature 'MChromatograms,Chromatogram'
alignRt(x, y, method = c("closest", "approx"), ...)

## S4 method for signature 'MChromatograms'
c(x, ...)

## S4 method for signature 'MChromatograms,missing'
compareChromatograms(
  x,
  y,
  ALIGNFUN = alignRt,
  ALIGNFUNARGS = list(),
  FUN = cor,
  FUNARGS = list(use = "pairwise.complete.obs"),
  ...
)

## S4 method for signature 'MChromatograms,MChromatograms'
compareChromatograms(
  x,
  y,
  ALIGNFUN = alignRt,
  ALIGNFUNARGS = list(),
  FUN = cor,
  FUNARGS = list(use = "pairwise.complete.obs"),
  ...
)

## S4 method for signature 'MChromatograms'
transformIntensity(object, FUN = identity)

Arguments

For `pData<-`: a `data.frame` with the number of rows matching
the number of columns of `object`.

For `colnames`: a `character` with the new column names.